Python for identifying minimal chromosomal regions among samples2019 Community Moderator ElectionProtected Execution EnvironmentMerge fields in a fileWriting a program for editing .txt data - Python or Unix?Nested 'awk' in a 'while' loop, parse two files line by line and compare column valuesInvoke python script through make commandWhy won't MOTD display output from a Python script it calls outside of /etc/update-motd.d/ unless it's in this directory?Running daemon involving GPIO on Piscript to parse file for two consecutive lines of unequal lengthErrors were encountered while processing: python-minimalhow to substitute strings in a set of files with different strings?
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Python for identifying minimal chromosomal regions among samples
2019 Community Moderator ElectionProtected Execution EnvironmentMerge fields in a fileWriting a program for editing .txt data - Python or Unix?Nested 'awk' in a 'while' loop, parse two files line by line and compare column valuesInvoke python script through make commandWhy won't MOTD display output from a Python script it calls outside of /etc/update-motd.d/ unless it's in this directory?Running daemon involving GPIO on Piscript to parse file for two consecutive lines of unequal lengthErrors were encountered while processing: python-minimalhow to substitute strings in a set of files with different strings?
I have multiple sample files (>20) that look like:
chr startpos endpos
1 14930 818094
1 818161 31595422
2 35593931 35865807
2 35868158 104785784
And I would like to output regions that are common among samples. E.g. if sample 1 has:
1 14900 818000
sample 2:
1 15000 605000
sample 3:
1 25000 705000
I would like to output:
1 25000 605000
I would also like to include a majority rule such that e.g if 10 out of totally 20 samples have a minimal region -> output the region. I.e. I would like to have it flexible how many samples that need to have the region for it to be printed to the output.
Does anyone have a python solution for this?
python bioinformatics
asked 12 hours ago
lindaklindak
72
add a comment |
I have multiple sample files (>20) that look like:
chr startpos endpos
1 14930 818094
1 818161 31595422
2 35593931 35865807
2 35868158 104785784
And I would like to output regions that are common among samples. E.g. if sample 1 has:
1 14900 818000
sample 2:
1 15000 605000
sample 3:
1 25000 705000
I would like to output:
1 25000 605000
I would also like to include a majority rule such that e.g if 10 out of totally 20 samples have a minimal region -> output the region. I.e. I would like to have it flexible how many samples that need to have the region for it to be printed to the output.
Does anyone have a python solution for this?
python bioinformatics
asked 12 hours ago
lindaklindak
72
2
This question is not really about Unix/Linux, but about programming (coding, algorithms) so it's more appropriate for Stack Overflow rather than this site.
– filbranden
10 hours ago
2
Also note that people at Stack Exchange will typically not want to do your work/homework for you. These are volunteers here, who are happy to help, but you need to show you're making an effort too. So try to solve this on your own and, when you get stumped, ask a question specific about what is happening that is unexpected. You're more likely to get useful answers (and to learn!) that way.
– filbranden
10 hours ago
add a comment |
I have multiple sample files (>20) that look like:
chr startpos endpos
1 14930 818094
1 818161 31595422
2 35593931 35865807
2 35868158 104785784
And I would like to output regions that are common among samples. E.g. if sample 1 has:
1 14900 818000
sample 2:
1 15000 605000
sample 3:
1 25000 705000
I would like to output:
1 25000 605000
I would also like to include a majority rule such that e.g if 10 out of totally 20 samples have a minimal region -> output the region. I.e. I would like to have it flexible how many samples that need to have the region for it to be printed to the output.
Does anyone have a python solution for this?
python bioinformatics
asked 12 hours ago
lindaklindak
72
I have multiple sample files (>20) that look like:
chr startpos endpos
1 14930 818094
1 818161 31595422
2 35593931 35865807
2 35868158 104785784
And I would like to output regions that are common among samples. E.g. if sample 1 has:
1 14900 818000
sample 2:
1 15000 605000
sample 3:
1 25000 705000
I would like to output:
1 25000 605000
I would also like to include a majority rule such that e.g if 10 out of totally 20 samples have a minimal region -> output the region. I.e. I would like to have it flexible how many samples that need to have the region for it to be printed to the output.
Does anyone have a python solution for this?
python bioinformatics
python bioinformatics
asked 12 hours ago
lindaklindak
72
asked 12 hours ago
lindaklindak
72
asked 12 hours ago
lindaklindak
72
asked 12 hours ago
lindaklindak
72
asked 12 hours ago
lindaklindak
72
72
2
This question is not really about Unix/Linux, but about programming (coding, algorithms) so it's more appropriate for Stack Overflow rather than this site.
– filbranden
10 hours ago
2
Also note that people at Stack Exchange will typically not want to do your work/homework for you. These are volunteers here, who are happy to help, but you need to show you're making an effort too. So try to solve this on your own and, when you get stumped, ask a question specific about what is happening that is unexpected. You're more likely to get useful answers (and to learn!) that way.
– filbranden
10 hours ago
add a comment |
2
This question is not really about Unix/Linux, but about programming (coding, algorithms) so it's more appropriate for Stack Overflow rather than this site.
– filbranden
10 hours ago
2
Also note that people at Stack Exchange will typically not want to do your work/homework for you. These are volunteers here, who are happy to help, but you need to show you're making an effort too. So try to solve this on your own and, when you get stumped, ask a question specific about what is happening that is unexpected. You're more likely to get useful answers (and to learn!) that way.
– filbranden
10 hours ago
2
2
This question is not really about Unix/Linux, but about programming (coding, algorithms) so it's more appropriate for Stack Overflow rather than this site.
– filbranden
10 hours ago
This question is not really about Unix/Linux, but about programming (coding, algorithms) so it's more appropriate for Stack Overflow rather than this site.
– filbranden
10 hours ago
2
2
Also note that people at Stack Exchange will typically not want to do your work/homework for you. These are volunteers here, who are happy to help, but you need to show you're making an effort too. So try to solve this on your own and, when you get stumped, ask a question specific about what is happening that is unexpected. You're more likely to get useful answers (and to learn!) that way.
– filbranden
10 hours ago
Also note that people at Stack Exchange will typically not want to do your work/homework for you. These are volunteers here, who are happy to help, but you need to show you're making an effort too. So try to solve this on your own and, when you get stumped, ask a question specific about what is happening that is unexpected. You're more likely to get useful answers (and to learn!) that way.
– filbranden
10 hours ago
add a comment |
1 Answer
1
active
oldest
votes
Not sure whether this a question for the Unix & Linux stackexchange. It sounds more like a general programming question.
However, I'd encourage you to look into using pandas.
You can import your sample file as a dataframe, specifying tab delineation as follows:
import pandas as pd
df = pd.read_csv('/tmp/samplefile.csv',sep='t')
If you know that startpos will always be smaller than endpos, you could find the output you're looking for by taking the maximum of df['startpos'] and the minimum of df['endpos'].
answered 10 hours ago
mttpgnmttpgn
18317
add a comment |
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1 Answer
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1 Answer
1
active
oldest
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active
oldest
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active
oldest
votes
Not sure whether this a question for the Unix & Linux stackexchange. It sounds more like a general programming question.
However, I'd encourage you to look into using pandas.
You can import your sample file as a dataframe, specifying tab delineation as follows:
import pandas as pd
df = pd.read_csv('/tmp/samplefile.csv',sep='t')
If you know that startpos will always be smaller than endpos, you could find the output you're looking for by taking the maximum of df['startpos'] and the minimum of df['endpos'].
answered 10 hours ago
mttpgnmttpgn
18317
add a comment |
Not sure whether this a question for the Unix & Linux stackexchange. It sounds more like a general programming question.
However, I'd encourage you to look into using pandas.
You can import your sample file as a dataframe, specifying tab delineation as follows:
import pandas as pd
df = pd.read_csv('/tmp/samplefile.csv',sep='t')
If you know that startpos will always be smaller than endpos, you could find the output you're looking for by taking the maximum of df['startpos'] and the minimum of df['endpos'].
answered 10 hours ago
mttpgnmttpgn
18317
add a comment |
Not sure whether this a question for the Unix & Linux stackexchange. It sounds more like a general programming question.
However, I'd encourage you to look into using pandas.
You can import your sample file as a dataframe, specifying tab delineation as follows:
import pandas as pd
df = pd.read_csv('/tmp/samplefile.csv',sep='t')
If you know that startpos will always be smaller than endpos, you could find the output you're looking for by taking the maximum of df['startpos'] and the minimum of df['endpos'].
answered 10 hours ago
mttpgnmttpgn
18317
Not sure whether this a question for the Unix & Linux stackexchange. It sounds more like a general programming question.
However, I'd encourage you to look into using pandas.
You can import your sample file as a dataframe, specifying tab delineation as follows:
import pandas as pd
df = pd.read_csv('/tmp/samplefile.csv',sep='t')
If you know that startpos will always be smaller than endpos, you could find the output you're looking for by taking the maximum of df['startpos'] and the minimum of df['endpos'].
answered 10 hours ago
mttpgnmttpgn
18317
edited 9 hours ago
answered 10 hours ago
mttpgnmttpgn
18317
answered 10 hours ago
mttpgnmttpgn
18317
answered 10 hours ago
mttpgnmttpgn
18317
18317
add a comment |
add a comment |
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2
This question is not really about Unix/Linux, but about programming (coding, algorithms) so it's more appropriate for Stack Overflow rather than this site.
– filbranden
10 hours ago
2
Also note that people at Stack Exchange will typically not want to do your work/homework for you. These are volunteers here, who are happy to help, but you need to show you're making an effort too. So try to solve this on your own and, when you get stumped, ask a question specific about what is happening that is unexpected. You're more likely to get useful answers (and to learn!) that way.
– filbranden
10 hours ago